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Lima

Demultiplex PacBio single-molecule sequencing reads

https://github.com/PacificBiosciences/barcoding

Lima, the PacBio barcode demultiplexer, is the standard tool to identify barcode sequences in PacBio single-molecule sequencing data. Starting in SMRT Link v5.1.0, it is the tool that powers the Demultiplex Barcodes GUI-based analysis application.

The module parses the report and count files generated by Lima, a PacBio tool to demultiplex PacBio single-molecule sequencing data.

By default, Lima will use barcode1--barcode2 as the sample names. To prevent these barcodes showing up in the General Statistics table of MultiQC, the Lima results are added to their own section.

If you want to include the Lima results in the General Statistics table, you can rename the barcode1--barcode2 filenames to their apropriate samples using the --replace-names option. Each sample that is specified in this way will be moved from the Lima section to the General Statistics table.

File search patterns​

lima/counts:
  contents: "IdxFirst\tIdxCombined\tIdxFirstNamed\tIdxCombinedNamed\tCounts\tMeanScore"
  num_lines: 1
lima/summary:
  contents: ZMWs above all thresholds
  max_filesize: 1024
  num_lines: 2